Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press A genomic portrait of the emergence, evolution and global spread of a methicillin resistant Staphylococcus aureus pandemic Matthew T.G. Holden1*, Li-Yang Hsu1,2, Kevin Kurt3, Lucy A. Weinert4,†, Alison E. Mather1, Simon R. Harris1, Birgit Strommenger3, Franziska Layer3, Wolfgang Witte3, Herminia de Lencastre5,6, Robert Skov7, Henrik Westh8,9, Helena Žemličková10, Geoffrey Coombs11, Angela M. Kearns12, Robert L.R. Hill12, Jonathan Edgeworth13, Ian Gould14, Vanya Gant15, Jonathan Cooke16, Giles F. Edwards17, Paul R. McAdam18, Kate E. Templeton19, Angela McCann20, Zhemin Zhou20, Santiago Castillo-Ramírez21, Edward J. Feil21, Lyndsey O. Hudson4, Mark C. Enright4,‡, 4, 4 4 18 Francois Balloux +, David M. Aanensen , Brian G. Spratt , J. Ross Fitzgerald , 1 20 1 3 Julian Parkhill , Mark Achtman *, Stephen D. Bentley , Ulrich Nübel *. 1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 2 National University Health System, 1E Kent Ridge Road, NUHS Tower Block Level 10, Singapore 119228, Singapore. 3 Robert Koch Institute, Wernigerode, Germany. 4 Department of Infectious Disease Epidemiology, Imperial College London, St. Mary’s Hospital Campus, London, UK. 5 Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal. 6 Laboratory of Microbiology, The Rockefeller University, New York, USA. 7 Statens Serum Institut, Copenhagen, Denmark. 8 Hvidovre Hospital, Hvidovre, Denmark. 9 University of Copenhagen, Faculty of Health, Copenhagen, Denmark. 10 National Institute of Public Health, Prague, Czech Republic. 11 Royal Perth Hospital, Perth, Western Australia. 12 Microbiology Services, Health Protection Agency, 61 Colindale Avenue, London, UK. 13 Department of Nephrology & Transplantation, King's College London, Guy's, King's & St Thomas' Medical School, Guy's Hospital, London, UK. 14 Aberdeen Royal Infirmary, Aberdeen, UK. 1 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press 15 University College London Hospital, London, UK. 16 Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK. 17 Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK. 18 The Roslin Institute and Edinburgh Infectious Diseases, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK. 19 Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK. 20 Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland. 21 Department of Biology and Biochemistry, University of Bath, South Building, Claverton Down, Bath, UK. † present address: University of Cambridge, UK. ‡ present address: University of Bath, UK. + present address: University College, London, UK. Running title: Drug resistance and the genesis of a MRSA pandemic Corresponding Authors: Ulrich Nübel, Robert Koch Institute, Burgstr. 37, 38855 Wernigerode, Germany. email: [email protected] Mark Achtman, Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland. email: [email protected] Matthew Holden, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. Email: [email protected] 2 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalised patients. Of particular concern are globally disseminated methicillin- resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with healthcare. The most rapidly spreading and tenacious healthcare- associated clone in Europe currently is EMRSA-15, a lineage that was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. To understand the genetic events that have accompanied the emergence of the EMRSA-15 pandemic, we obtained genome sequences for 193 isolates that were chosen for their geographical and temporal diversity, and belong to the same multilocus sequence type as EMRSA-15. Using phylogenomic methods, we were able to show that the current pandemic population of EMRSA-15 descends from a healthcare-associated MRSA epidemic that spread through England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 sub-clone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this sub-clone over the last twenty years has grown four times faster than its progenitor. Using comparative genomic analysis we were able to identify the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital 3 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens. Introduction Methicillin-resistant Staphylococcus aureus (MRSA) remains a major global cause of healthcare-associated infections since it was first described five decades ago following the introduction of penicillinase-stable β-lactam antibiotics into clinical practice (Klein et al. 2007). During this period, MRSA strains have emerged several times by acquiring variants of staphylococcal cassette chromosome mec (SCCmec) elements that carry the mecA methicillin-resistance determinant (Robinson and Enright 2003; Nübel et al. 2008). However, the vast majority of MRSA isolated worldwide belong to a limited number of clones, some of which are associated with global epidemics. Epidemic MRSA-15 (EMRSA-15) has proven to be particularly successful over the last two decades, transmitting rapidly within and between hospitals, as well as to different countries. EMRSA-15 carries a type IV SCCmec element, and belongs to multilocus sequence type ST22. Initially isolated in the south-east of England in 1991 (Richardson and Reith 1993), the spread of EMRSA-15 in the UK healthcare setting was rapid; by 2000, EMRSA-15 accounted for over 60% of MRSA nosocomial bacteremias in England (Johnson et al. 2001). Over this period the proportion of MRSA among S. aureus bacteremia in the UK increased from less than 2% to 40% (Johnson et al. 2001). 4 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Shortly after EMRSA-15 was reported in England, MRSA indistinguishable from EMRSA-15 were reported to cause outbreaks in other geographic regions, including Germany, the Czech Republic, Portugal, New Zealand, Australia, and Singapore (Pearman et al. 2001; Witte et al. 2001; Hsu et al. 2005; Melter et al. 2006; Amorim et al. 2007; Grundmann et al. 2010). These belong to multilocus sequence type ST22 or its close relatives. In a recent structured survey, ST22 was the most frequently found MRSA across Europe (Grundmann et al. 2010), and it was among the three most frequent MRSA clones in seven out of 15 countries for which quantitative data were available (Grundmann et al. 2010). Although reported in many countries, ST22- MRSA accounted for only 0.2% of MRSA in a surveillance study recently performed in the USA (Limbago et al. 2009) and has not, as yet, been reported from South America (Sola et al. 2008) and from large parts of Asia (Arakere et al. 2005; Ko et al. 2005). ST22-MRSA has repeatedly demonstrated its ability to supplant and replace other, formerly established MRSA strains (Hsu et al. 2005; Amorim et al. 2007; Aires-de-Sousa et al. 2008; Witte et al. 2008). Of further concern, ST22-MRSA containing the lukS/F genes (encoding the Panton Valentin leucocidin) has been reported to cause community-associated infections (Linde et al. 2005; Witte et al. 2007). The mechanisms that lead to the emergence and spread of MRSA strains are of great interest. Despite intense research in this area, the spatiotemporal dynamics of the population structure and epidemic spread remain poorly understood, partially due to the limited resolution provided by contemporary genotyping tools. In this study we have investigated the origins and evolution of EMRSA15 by whole genome sequencing 193 ST22 isolates from 15 countries collected between 1990 and 2009. 5 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Integrating evolutionary and spatial information, we have reconstructed the spatial and temporal dynamics underpinning the expansion of this clone, and ascertained the genetic changes correlating with its enhanced spreading success. 6 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Results Phylogenomic reconstruction of the ST22 lineage. We determined full genome sequences from 193 ST22 isolates (Supplemental Table S1), including isolates both from hospital and community settings,